From cce3a8c9c720c01c40752fba40a1a0f175fc498d Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 31 Jan 2018 17:00:34 +0000
Subject: [PATCH] store link to NCBIGene where available
---
.../XrefParser/RefSeqCoordinateParser.pm | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
index daf0b1e557..92a4c79391 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
@@ -208,6 +208,11 @@ sub run_script {
return;
}
+## Add link to EntrezGene IDs where available
+ my (%entrez_ids) = %{ $self->get_valid_codes("EntrezGene", $species_id, $dbi) };
+ my $entrez_source_id = $self->get_source_id_for_source_name('EntrezGene', undef, $dbi);
+ my $add_dependent_xref_sth = $dbi->prepare("INSERT INTO dependent_xref (master_xref_id,dependent_xref_id, linkage_source_id) VALUES (?,?, $entrez_source_id)");
+
my $sa = $core_dba->get_SliceAdaptor();
my $sa_of = $otherf_dba->get_SliceAdaptor();
my $chromosomes_of = $sa_of->fetch_all('toplevel', undef, 1);
@@ -371,13 +376,23 @@ sub run_script {
info_type => 'DIRECT' });
$self->add_direct_xref($xref_id, $best_id, "Transcript", "", $dbi);
-# Also store refseq protein as direct xref for ensembl translation, if translation exists
my $ta_of = $otherf_dba->get_TranscriptAdaptor();
my $t_of = $ta_of->fetch_by_stable_id($id);
+ my $g_of = $t_of->get_Gene();
+ my $entrez_id = $g_of->stable_id();
my $tl_of = $t_of->translation();
my $ta = $core_dba->get_TranscriptAdaptor();
my $t = $ta->fetch_by_stable_id($best_id);
my $tl = $t->translation();
+
+# Add link between Ensembl gene and EntrezGene
+ if (defined $entrez_ids{$entrez_id} ) {
+ foreach my $dependent_xref_id (@{$entrez_ids{$entrez_id}}) {
+ $add_dependent_xref_sth->execute($xref_id, $dependent_xref_id);
+ }
+ }
+
+# Also store refseq protein as direct xref for ensembl translation, if translation exists
if (defined $tl && defined $tl_of) {
if ($tl_of->seq eq $tl->seq) {
($acc, $version) = split(/\./, $tl_of->stable_id());
--
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